Pokemon: Chosen Paths
by Anonymouswriter10000
Summary: In an alternate timeline, the rules of the Pokemon world have been turned on their head! Welcome to the world of Pokemon, where epic heroes, vile villans, and an insane desert wanderer will determine the fate of the universe!


Chapter 1: Pilot/The Grim Future

By now, you probably know of the theory that Pokemon Generations 1-5 and Generation 6/The Remakes take place on different timelines. One timeline where the secret of mega evolution was discovered, one where it wasn't. But what if I told you there was yet another fork in the road, one where Mega Evolution had been discovered even before the invention of Poke Balls, when warlords fought valiantly for their kingdoms and people couldn't rely on the power of machines? In a world where Mega Evolutions would seem the least possible, the powers hidden in the cores of the Mega Stones would shape the course of history even more so than in any other variation of the Pokemon world's history.

In this world, Pokemon ran feral, and were only tamable either when they were very young or by those who were cruel enough to break the spirits of the great beasts. As I mentioned, Poke Balls never graced this land, so Pokemon walked freely with their masters, forming strong bonds with their partners/masters. Some could even form a bond with their Pokemon strong enough to trigger a premature Mega Evolution, but this would only be possible if the Pokemon and master decide to undergo the commitment. However, there are special cases where it is forced by a deity in order for them to achieve their goals. Nonetheless, these masters of Megas were respected as living gods, and where given by a sage mega evolution master named Londenn, another chosen one, a Mega Stone and Key Stone to help trigger the evolution, as well as keep the massive shockwave that resulted under control. These "Chosen Ones", however, were also trusted with the protection of the known world.

The mysterious Mega Stones came from Rayquaza, who brought them down from the heavens to assist humanity in its fight for survival against other species. Rayquaza was the most widely worshipped god in all of the kingdoms. (Even those who lived in the wastelands would often say a prayer to Rayquaza before beginning the day) Humanity respected Rayquaza's power for a long time… but eventually, a few of the chosen ones began to envy the Ozone Titan's power, and believed that Rayquaza's power was rightfully theirs. One especially foolish Chosen One even had the gall to attack Rayquaza, eventually causing the Air Lock pokemon to retreat into space.

This significant, heartbreaking but seemingly harmless event came with the horrifying side effect of releasing Primal Groudon and Kyogre onto the world.

A long, bloody war against the clashing Primals ensued. Many Chosen Ones and their Pokemon partners lost their lives, and eventually, the entire world fell into ruin. At this point, even the gods have given up on the forsaken hole of this world, and have left the remaining people to fight off their fates. However, some pockets of civilization still survived, fighting for their right to go on with the last of their hopes.

And it is in one of these pockets that our story begins…

Somewhere on the coast of the Middle Sea…

"I thought I could finally wash off these dirt marks… But the water is still as hot as Charizard's breath," sighed a young man named Grey. He is one of the last surviving humans – no, living beings on this planet. Although he is a tad weak, his mind is truly something that can only be born once in a century. Grey's intelligence and keen interest in Mega Evolution led to him creating the first 2 artificial Mega-Evolving Pokemon in the history of this world.

These two Pokemon are technically of the same species, but in the same column as Charizard, it has two different Mega forms. Grey created a pair of Mewtwo by extracting the DNA from a piece of fur that Mew, one of the last deities that stayed in this world, dropped as it flied off, never to return. At the time when Grey's Mewtwo creation process started, he was living in a bunker underneath Mt. Jaune. It was a fairly comfortable setting (if you didn't count the constant fear that you'd never wake up from sleeping), with a few hay bales serving as beds and a makeshift fireplace constructed out of rubble and Spinarak thread. Due to the bunker being deep below the ground, it was a very pleasant temperature, which kept the sanity of Grey and his friend.

As for Grey's friend, it was a lone human partner named Lustre. See, in the future, the names given to the people are almost always based off of descriptive words that describe something very important to the givers of said names. In this case, her parents due to their hopes named her Lustre for a bright, lustrous future where they'd never had to worry about the ongoing apocalypse. However, a wild Ursaring slaughtered Lustre's parents, in front of her, when she was 6, and she became an orphan. Very fortunately for her, however, Grey found the girl while he was hunting for fresh Deerling meat, at around a day after Lustre's parents left the world.

Over time, the two have become an inseparable duo, overcoming all obstacles thrown at them, whether it is an earthquake, flood, or anything in between. They have saved each other's backs over and over again to a point that it would be a sin if one were to fail in their duty to protect the other. It was crucial to survival in the bleak future, because if you were alone, you would be dead unless you had the mind that Grey possessed.

With Grey's vast knowledge and overall mental strength, he was also able to develop the best of technologies with a few rods of metal, wire, tree branches and Spinarak thread. Such examples of said technologies were weaponry to fend off the permanently agitated Pokemon of the future, tools to ensure that food was free of Pokerus, a dangerous virus in this universe, and even a cloning lab deep inside the bunker, where the creation of the two Mewtwos took place.

Once the cloning was complete, the two Mewtwos were completely blank slates. They had no personality whatsoever except for the primitive instincts of the Mew. To them, Grey was like a busy father and Lustre became their mother figure, tending to them when Grey was off hunting for food. The Mewtwos, however, were created so that food was only consumed as a simple pleasure. They had no real need for food, water, or sleep, at least for a very long time. What the Mewtwos really needed to survive was to not sustain any major injuries. Due to cloning still being very experimental, even in the hands of geniuses like Grey, Mewtwo genes are actually very unstable, and should not be exposed to large doses of Infinity Energy, the thing that fuels Mega Evolution, and Primal Reversion, because that leads to a point of no return, where not even the gods can restore them.

Grey realized this major issue before their conception, and hit the books in a search for living beings that could not be exposed to Infinity Energy. Fortunately, he found a book titled "Londenn and Lucario" in Lustre's bookshelf. It noted little things like Londenn's bond with his Lucario, and other stuff, but that wasn't what Grey was searching for. The interest kicked in when he saw a chapter titled "Infinite Instability", stating that his Lucario was unable to utilize its Mega Stone lest it goes wild in the Mega form. However, upon closer reading, Grey learned that it was able to be completely nullified through an opposite form of Infinity Energy. This form of Infinity Energy was known as Infinity X Energy or Infinity Y Energy. All living things exert one of the two energies, except Mega Rayquaza (and Zygarde, another god, which exerts both of them.)

This discovery led to Grey figuring out that each energy emitted a type of wave, each with different amplitudes, one intensely positive and one intensly negative, as well as the fact that one can cancel the other out to eradicate any instability, and with a power amplification of a factor of two. Knowledge of this was applied to the Mewtwo by looking into the wavelengths emitted by each of them. The Mewtwo with an X wavelength was crafted a Mega Stone emitting Y energy, and vice versa. At the end, Grey and Lustre had their first Pokemon, though artificial, companions.

Which leads us to now.

Grey and Lustre are in the middle of a buggy ride after stopping at a small stream, with their Mewtwo partners in tow. There were provisions, including some smoked Goldeen, Combee honey, bread, Sitrus and Lum Berries, and a large container of water. The buggy may have been a bit rocky at times, but it was very luxurious considering that the world was a very dangerous place. Seas became death traps that sucked you in if you went past shallow water, the sky was almost always cloudy, every mountain had the risk of becoming a volcano the next day and standing near a tectonic plate border for over a day was considered suicide.

The previous home of Grey, Mt. Jaune, was no exception to the natural calamities that the Primals' clash would bring forth. Even the calmness of the peak was shattered eventually, and much of the lifeforms on Mt. Jaune were eradicated once the top erupted with molten rock and ash. Beyond the uppermost reaches of the ashes was a huge discharge of energy – not electricity, but Infinity Energy of unknown wavelength. Due to the outburst of said energy, the surviving Pokemon became much more dangerous, intelligent and powerful due to the high chance of two wavelengths being the same. It was only natural that Grey and Lustre would have to escape the bunker before they became cornered.

After a long ride, the group arrived at another mountain by the name of Mt. Vert. This mountain has been affected by mass flooding due to being closer to water than other places like Mt. Jaune, but the top parts were untouched by natural disasters. Lustre got off first, unloaded the makeshift tents and the Mewtwo helped set it up, although they preferred to sleep on a tree, or under a rock instead of with their masters. Perhaps it was just a part of them wanting solitude, but regardless of reason, Grey and Lustre were fine with letting them roam free.

Once set up, Lustre gets up and says to Grey, "We didn't bring a lot of food with us, did we?"

"Hmm," Grey hummed. "It does appear that we may not have packed enough food. Would you mind hunting for some berries and Pokemon?"

"But I already went hunting last time, Grey! You go do it this time, I'd rather rest up with the Mewtwo."

"Normally, I'd agree with you," Grey replied. "but this time, I have to continue working on my special machine. I'll tell you about it when it's almost done, because I.. I think this creation will be revolutionary."

"Well, you've never been wrong when it came to you working on some sort of machine," Lustre sighed. "Fine, pass me the tranquilizer. X, come with me please, we're gonna go hunting!" X , one of the Mewtwos, got up without a word, and followed her into the Mt. Vert forest (which the mountain had a lot of, giving it its name). Grey continued tinkering with his tools and parts, with a small energy pistol by his right side and Y, the other mewtwo, keeping close watch on him.

About an hour or two later, Grey gets up with a satisfied but mucky smile on his face. He has built a strange radar machine out of an old microwave motherboard and a calculator, but it was unclear to an average person as to what this would be used to detect. This was especially true to Lustre, who had just come back from a long hunt in the bush, with X lugging around a Deerling corpse, some Fletchinder meat and the hide of an Electrike that had a dart sticking outside its back. Grey's side of things wasn't completely unproductive either if you don't count his machine tinkering. There was a dead Ursaring laying around Mewtwo Y after it tried to attack Grey for unknown reasons, possibly because it was in a frenzy after being affected by the Infinity Energy discharge at Mt. Jaune, or that it felt its territory was being invaded. Regardless of reason, it simply lay there, motionless.

"So, I see you've done some hunting on your own, huh, Grey?" Lustre asked.

"Hey, that thing was hunting me! Thankfully, Y was close by, guarding me from potential Grey-killers like that Ursaring."

"To be fair, nothing really stands a chance against the Mewtwo you've created," Lustre said. "They're really as strong as the original god, Mew."

"That's all I ever wanted. Though they may not be as passionate as Mew seemed to be, from what I hear anyways, they really do have a heart that cares about us. And I don't plan to betray their trust any time soon."

"Neither do I. However, where should we dump the stuff I got? Can't wait to have a tasty Fletchinder breast tonight, it's been a long time since we've eaten a hot meal, if you get what I'm saying."

"Of course I do. Fletchinder is a fire type, after all. Don't think I can't understand your humour, especially since it's been years living with you!"

"I'm also curious… What's that machine you're holding in your hands?"

"This? It's… It's a radar. The hope is that it can track Celebi down. I want to get us four into a better place. At this time period, however, it's impossible, and the chances get even lower if we dawdle around in our time."

"Celebi? Isn't that the weird onion looking thing that can travel through time? Grey, you're trying to bring us to a time where things are better? That's so nice of you, I can't be excited enough!"

"Don't get too excited, this is purely experimental. Don't get your hopes up too high, because there's a chance that this may not work."

"I think it'll work, Grey. Everything you do is perfect- Y, what is it?"

Y was pointing to a small shrine in the distance. It was unnoticeable to Grey and Lustre, but the X could feel it as well. The radar also began to point in the same direction as Y's finger, which meant that something was clearly going on at the shrine. Our little group of four packed everything into the buggy quickly, and drove off to the shrine with no regard for anything that could go wrong.

Upon arriving at the shrine, Grey's radar is beeping unbearably loudly. Could it be? Perhaps, this Celebi they were looking for was closer to them than they thought. Without hesitation, all four leapt off the buggy and entered the clearing where the shrine would be.

When they ran in, it was immediately apparent that there was indeed an onion shaped "thing" with an air of awe. However, it was in a lot of trouble. Immobilized by Ariados thread, Celebi struggled to even move itself, and the fact that the Ariados were agitated and coming closer to Celebi did not help the case at hand. To make things worse, the Ariados were firing Mud Shots and Poison Stings mercilessly at Celebi, slowly killing it.

"Lustre, we have to help it! If not, there's no way we can find a way back!" shouted Grey. Without stopping to think about the situation, Grey and Lustre grabbed a pistol each and fired at the oncoming Ariados. Although the onslaught of Ariados was stopped by the reckless efforts of Grey and Lustre, there was too much thread entrapping Celebi. Not even the sharpest knife in Grey's belt was able to rip through the tough thread easily. Celebi still had a scared expression on its face, but was starting to warm up a bit more, thinking it would be safe with its saviors standing by.

Grey knew that his knife wasn't able to cut the thread without difficulty, but his determination was fierce. He didn't stop, even if the thread tangled his knife, because he knew this was his only way to get to the past, where there was still a future. As usual, Lustre would stand by with the Mewtwo, occasionally dropping by Celebi and asking how it was doing. Celebi would respond with either silence, or a small squeak, but Lustre knew it was all pure gratitude.

After a surprisingly long amount of time, Grey's knife finally cut through the last of the Ariados thread. Celebi took no time to fly for joy, and took a minute to stop and stare at the people who saved it. As it flied off, Lustre shouted, "Celebi, may we please borrow your powers to travel through time?"

Celebi stopped, floated around in a small figure 8 and stopped moving around. Immediately after, it used its psychic powers to bring everyone together, even the Mewtwos and with a smile on its face, dragged the group to the past, where Celebi always loved to go when it felt down.

Grey awoke in a on a cobblestone floor. He shook himself quickly awake, and looked around. He was in a quaint little stone room, with a fire blazing in the fireplace, and a small table covered in the supplies in the middle. Lustre was still fast asleep in a nearby cot, and the Mewtwos were out like lights on the floor.

Grey's attention snapped to a nearby door, as a little old lady came in.

"Good morning, dear! Sorry you got the floor, but I thought the lady might need the cot more than you," the kind woman beamed.

"It's fine. She doesn't care where she sleeps, but she deserves it, she's been through a lot," Grey said, still half asleep.

"Aww, that's nice of you," the lady said. "Erm, sorry to ruin the moment, but do you have your rent ready? The gentleman who brought you in said that the rent would be paid this morning."

Grey flinched. He searched his person. There was no currency in the future, and even if there was, would it be valid in what he assumed was the past?

All of a sudden, a coin came flipping out of the darkness in the corner of the room, which Grey caught, and handed to the lady. "That should cover their room and board, Donna," a Cockney-accented voice spoke. "Can we have a minute alone and some breakfast as well, please?" the voice said, as a significantly larger coin came hurtling out of the shadows.

Donna caught the coin, and, with a smile, saw herself out.

The stranger leaned forward on his chair, exposing only a large, almost Chesire grin. "So, what's your story, sleepyhead?"


End file.
